random_forest_plot: random_forest_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

random_forest_plot

Description

Plots the importance of otu on predicting/classifying the sample_group and the accuracy using core otu, non-core otu and all otu.

Usage

random_forest_plot(
  otu,
  sample,
  mini_abun,
  threshold,
  sample_name,
  sample_group
)

Arguments

otu	a community count data matrix with samples in rows and OTUs/taxa in column,
sample	a sample information data.frame. The rownames must match the sample names in the otu,
mini_abun	a value indicating whether the otu is present,
threshold	a value indicating the final percent increase in beta-diversity,
sample_name	the name of a column that containing the sample name,
sample_group	the name of a column that containing the sample type/group,

Details

Plots the importance of otu on predicting/classifying the sample_group and the accuracy using core otu, non-core otu and all otu.

Value

A bar plot showing importance of otu on predicting/classifying the sample_group and a bar plot showing the accuracy using core otu, non-core otu and all otu.

Examples

 random_forest_plot(otu, sample, mini_abun=0, threshold=0.02, sample_name, sample_group)

lindan1128/coreMicrobiome documentation built on May 5, 2022, 8:24 p.m.